Just drop the books from the Kobo, ensure they are flagged correctly with Calibre (ie series and series #) and then upload away

Thank you, this did work!

However I did get 'unable to open database file' errors when I tried to do more than 1 change at a time. I think I'll just delete my library and start over again, will probably go faster in the long run. But at least the code is there and it will be all sorted the way I want when I'm done, so thank you again!